As the High Court sided this week with the National Secular Society, it ruled in a moment of sheer petty nastiness that having a moment for entirely voluntary prayers as part of a council's agenda was illegal. Pickles fired back that the "right to worship is a fundamental and hard fought British liberty" and promised that the general power of competence in his Localism Bill would overrule this.

I hope the general public is listening, and I hope other Conservatives are taking heed. With each victory that militant secularism celebrates, Conservatives should feel obliged by our principles and electoral necessity to defend religious liberty.

It is scarcely necessary to enumerate the many examples of injustices recently inflicted on Christians and others by the courts or the liberal-left. But there are many. People have faced losing their jobs for wearing a cross around their neck or placing one on the dashboard of their van. Doctors have been disciplined for mentioning their faith at work. A couple stood trial for describing the burkha as "oppressive". A teenager was tried for saying that Scientology is a "cult". A Warwickshire Mayor was officially reprimanded and forced to apologise to the press last month for describing Halloween as a "pagan festival" – apparently as it might offend pagans. A Lancashire café owner was told by police he was breaking the law by showing a DVD that featured the text of the Bible, one verse after another.

It should be said immediately that one does not have to be a conservative to be opposed to much of the above. Many decent people on the left would oppose the lack of proportion.

But at the heart of such measures is the growth of a militant secularism of the Richard Dawkins/Evan Harris variety. As this approach becomes the common sense of elites across the institutions, religious people are increasingly being pushed around.

So often, this militant secularism wears the cloak of the ancient principles of religious tolerance and liberty, put so well by Elizabeth I when she expressed "no desire to make windows into men's souls". But the notion of the state protecting everyone's right to pray to whomever and believe whatever they wish is a world away from much modern, extreme secularism. This attitude holds that public religious expression is suspect, that separation between church and state – including how taxpayers' money is spent – must be absolute, and that the emanations of the state should constantly be monitoring religious people or institutions, ever ready to crack down upon the slightest departure from this stringent policy.

This is an approach inherently unconservative in its absolutism, its ahistoricism, its lack of pragmatism and its view of the relationship between the state and the subject or citizen.

The last of these points deserves particular elaboration. Every militant secularist sees faith schools as a bad thing, irrespective of how much better they so often perform than secular schools. It should come as no surprise that it is religious groups that have done so much to make academies work – and, one hopes, free schools in time.

The justification is always phrased the same way: 'the state should not be funding religious education'. The problem is that, as every conservative knows, the state has no money. Every penny government ministers spend comes from taxpayers. "How very dare taxpayers presume to second-guess how the state spends its hard-earned money?!" is just about consistent with old-school socialism, but it is not a principle to which any conservative should subscribe. Indeed, many church schools were in the education business long before the state took them over. What could be a clearer infringement of liberty than the state banning religion from church institutions having nationalised them?

Other secularists appeal to a sense of fairness, suggesting that militant secularism is a neutral position. But as a friend put it to me recently, arguing that this secularism is the state taking a neutral stance on religion is like claiming that mandating nudity is the state taking a neutral stance on clothing. The secularism of the National Secular Society bans not clothes but faith schools of every variety. It mandates that all welfare and all aid be delivered through secular institutions, however ineffectively. It bans government support for religious rehabilitation programmes in prison. It would dismantle the Coronation and, as David Jones MP has suggested, prevent prayers in Parliament. As we saw above, it also leads inevitably to a thousand acts of pettiness that inflict needless harm on so many who did nothing more than wear a cross or pray for a patient.

Far from being a neutral stance on religion, militant secularism is a kind of aggregate of the intolerance of all religious bigots. Instead of leaving well alone all voluntary and harmless religious expression – my preferred model – modern secularism empowers the Christian bigot who supposedly "might be offended" if a Jewish school is founded in his borough, or the Muslim bigot who "might be offended" if his doctor wears a cross. Militant secularism gives enormous weight to these views and enforces this intolerance against everyone. Would that we could instead simply tell intolerant people to grow up.

Eric Pickles was right to speak out for another reason: pure politics.

Militant secularism is the doctrine of a tiny metropolitan few. As one senior Liberal Democrat admitted to me, it proved electorally lethal even in Oxford West. Scrapping church schools especially would be obvious electoral suicide in constituencies across the country – not for nothing has as keen a secularist as Ed Miliband unambiguously rejected this policy. As a party, we run very few risks by opposing this new secularism fiercely.

But there are a lot of Christians out there. 15% of the country continues to attend church at least monthly, with another 10% attending "occasionally". Notably, the bias of church attendance is towards older and wealthier sections of society. These are categories of people with higher than average turnout, so as a percentage of people who actually vote it will be even higher than this 15% to 25%. There is also a strong bias towards women, among whom the party has done especially badly in recent years.

Standing up for religious liberty is right in itself, but it will also be attractive to this important section of the electorate. Protecting religious liberty could be as politically potent as defending the right of non-believers not to pray, were they forced. Few will vote on religious freedom alone. But we will do better with many of these voters the more that Conservatives take up the cause of religious freedom in a way the other parties have not. Having done this, we should not be above pointing out to churchgoers that Labour politician who had nothing to say when their local doctor was disciplined for wearing a cross, or that Liberal Democrat who wants the local church school closed – and reaping the substantial electoral rewards.